1 package jalview.gui.structurechooser;
3 import java.util.Locale;
5 import java.util.ArrayList;
6 import java.util.Arrays;
7 import java.util.BitSet;
8 import java.util.Collection;
9 import java.util.Collections;
10 import java.util.Comparator;
11 import java.util.List;
13 import jalview.datamodel.SequenceI;
14 import jalview.fts.api.FTSData;
15 import jalview.fts.core.FTSRestRequest;
17 public class TDBResultAnalyser
21 * model categories - update as needed. warnings output if unknown types
24 * Order denotes 'trust'
26 private static List<String> EXP_CATEGORIES = Arrays
28 { "EXPERIMENTALLY DETERMINED", "DEEP-LEARNING", "TEMPLATE-BASED",
29 "AB-INITIO", "CONFORMATIONAL ENSEMBLE" });
31 private SequenceI seq;
33 private Collection<FTSData> collectedResults;
35 private FTSRestRequest lastTdbRequest;
43 private int idx_mqual;
45 private int idx_resol;
50 private String filter = null;
53 * limit to particular source
55 private String sourceFilter = null;
57 private int idx_mprov;
59 public TDBResultAnalyser(SequenceI seq,
60 Collection<FTSData> collectedResults,
61 FTSRestRequest lastTdbRequest, String fieldToFilterBy,
65 this.collectedResults = collectedResults;
66 this.lastTdbRequest = lastTdbRequest;
67 this.filter = fieldToFilterBy;
68 this.sourceFilter = string;
69 idx_ups = lastTdbRequest.getFieldIndex("Uniprot Start");
70 idx_upe = lastTdbRequest.getFieldIndex("Uniprot End");
71 idx_mcat = lastTdbRequest.getFieldIndex("Model Category");
72 idx_mprov = lastTdbRequest.getFieldIndex("Provider");
73 idx_mqual = lastTdbRequest.getFieldIndex("Confidence");
74 idx_resol = lastTdbRequest.getFieldIndex("Resolution");
78 * maintain and resolve categories to 'trust order' TODO: change the trust
79 * scheme to something comprehensible.
82 * @return 0 for null cat, less than zero for others
84 public final int scoreCategory(String cat)
90 String upper_cat = cat.toUpperCase(Locale.ROOT);
91 int idx = EXP_CATEGORIES.indexOf(upper_cat);
94 System.out.println("Unknown category: '" + cat + "'");
95 EXP_CATEGORIES.add(upper_cat);
96 idx = EXP_CATEGORIES.size() - 1;
98 return -EXP_CATEGORIES.size() - idx;
102 * sorts records discovered by 3D beacons and excludes any that don't
103 * intersect with the sequence's start/end rage
107 public List<FTSData> getFilteredResponse()
109 List<FTSData> filteredResponse = new ArrayList<FTSData>();
111 // ignore anything outside the sequence region
112 for (FTSData row : collectedResults)
114 int up_s = (Integer) row.getSummaryData()[idx_ups];
115 int up_e = (Integer) row.getSummaryData()[idx_upe];
116 String provider = (String) row.getSummaryData()[idx_mprov];
117 String mcat = (String) row.getSummaryData()[idx_mcat];
118 // this makes sure all new categories are in the score array.
119 int scorecat = scoreCategory(mcat);
120 if (sourceFilter == null || sourceFilter.equals(provider))
122 if (seq == row.getSummaryData()[0] && up_e > seq.getStart()
123 && up_s < seq.getEnd())
125 filteredResponse.add(row);
129 // sort according to decreasing length,
131 Collections.sort(filteredResponse, new Comparator<FTSData>()
134 public int compare(FTSData o1, FTSData o2)
136 Object[] o1data = o1.getSummaryData();
137 Object[] o2data = o2.getSummaryData();
138 int o1_s = (Integer) o1data[idx_ups];
139 int o1_e = (Integer) o1data[idx_upe];
140 int o1_cat = scoreCategory((String) o1data[idx_mcat]);
141 String o1_prov= ((String) o1data[idx_mprov]).toUpperCase(Locale.ROOT);
142 int o2_s = (Integer) o2data[idx_ups];
143 int o2_e = (Integer) o2data[idx_upe];
144 int o2_cat = scoreCategory((String) o2data[idx_mcat]);
145 String o2_prov= ((String) o2data[idx_mprov]).toUpperCase(Locale.ROOT);
148 if (o1_cat == o2_cat)
152 int o1_xtent = o1_e - o1_s;
153 int o2_xtent = o2_e - o2_s;
154 if (o1_xtent == o2_xtent)
156 if (o1_cat == scoreCategory(EXP_CATEGORIES.get(0)))
158 if (o1_prov.equals(o2_prov)) {
159 if ("PDBE".equals(o1_prov)) {
160 if (eitherNull(idx_resol,o1data,o2data))
162 return nonNullFirst(idx_resol,o1data,o2data);
164 // experimental structures, so rank on quality
165 double o1_res = (Double) o1data[idx_resol];
166 double o2_res = (Double) o2data[idx_resol];
167 return (o2_res < o1_res) ? 1 : (o2_res == o1_res) ? 0 : -1;
169 return 0; // no change in order
172 // PDBe always ranked above all other experimentally determined categories
173 return "PDBE".equals(o1_prov) ? -1 : "PDBE".equals(o2_prov) ? 1 : 0;
178 if (eitherNull(idx_mqual,o1data, o2data)) {
179 return nonNullFirst(idx_mqual, o1data, o2data);
181 // models, so rank on qmean - b
182 double o1_mq = (Double) o1data[idx_mqual];
183 double o2_mq = (Double) o2data[idx_mqual];
184 return (o2_mq < o1_mq) ? 1 : (o2_mq == o1_mq) ? 0 : -1;
189 return o1_xtent - o2_xtent;
199 return o2_cat - o1_cat;
203 private int nonNullFirst(int idx_resol, Object[] o1data,
206 return o1data[idx_resol] == o2data[idx_resol] ? 0: o1data[idx_resol] != null ? -1 : 1;
209 private boolean eitherNull(int idx_resol, Object[] o1data,
212 return (o1data[idx_resol] == null || o2data[idx_resol]==null);
216 public boolean equals(Object obj)
218 return super.equals(obj);
221 return filteredResponse;
225 * return list of structures to be marked as selected for this sequence
226 * according to given criteria
228 * @param filteredStructures
229 * - sorted, filtered structures from getFilteredResponse
232 public List<FTSData> selectStructures(List<FTSData> filteredStructures)
234 List<FTSData> selected = new ArrayList<FTSData>();
235 BitSet cover = new BitSet();
236 cover.set(seq.getStart(), seq.getEnd());
237 // walk down the list of structures, selecting some to add to selected
238 // TODO: could do simple DP - double loop to select largest number of
239 // structures covering largest number of sites
240 for (FTSData structure : filteredStructures)
242 Object[] odata = structure.getSummaryData();
243 int o1_s = (Integer) odata[idx_ups];
244 int o1_e = (Integer) odata[idx_upe];
245 int o1_cat = scoreCategory((String) odata[idx_mcat]);
246 BitSet scover = new BitSet();
247 // measure intersection
248 scover.set(o1_s, o1_e);
250 if (scover.cardinality() > 4)
252 selected.add(structure);
253 // clear the range covered by this structure
254 cover.andNot(scover);
257 if (selected.size()==0)
261 // final step is to sort on length - this might help the superposition
263 Collections.sort(selected, new Comparator<FTSData>()
266 public int compare(FTSData o1, FTSData o2)
268 Object[] o1data = o1.getSummaryData();
269 Object[] o2data = o2.getSummaryData();
270 int o1_xt = ((Integer) o1data[idx_upe])
271 - ((Integer) o1data[idx_ups]);
272 int o1_cat = scoreCategory((String) o1data[idx_mcat]);
273 int o2_xt = ((Integer) o2data[idx_upe] - (Integer) o2data[idx_ups]);
274 int o2_cat = scoreCategory((String) o2data[idx_mcat]);
275 return o2_xt - o1_xt;
279 ThreeDBStructureChooserQuerySource.FILTER_FIRST_BEST_COVERAGE))
281 return selected.subList(0, 1);